OK - I am cleaning out my draft blog post list. I start many posts and don't finish them and then they sit in the draft section of blogger. Well, I am going to try to clean some of that up by writing some mini posts. Here is #2:

Saw an interesting story on Genome Web: 'Denizens' of the Deep | The Daily Scan | GenomeWeb. I have not been able to get the original article yet, but it seems that what they have done can basically be considered metagenomics for animals. They collected sloughed off cells and other material from a lake and surveyed it for animal DNA. This seems like a very cool derivative of metagenomic approaches and has enormous potential. But alas, I never got down to getting access to the paper: Monitoring endangered freshwater biodiversity using environmental DNA so this will have to stay as a mini post. Damn non open access journals ...

OK - I am cleaning out my draft blog post list. I start many posts and don't finish them and then they sit in the draft section of blogger. Well, I am going to try to clean some of that up by writing some mini posts. Here is the first ---

Thursday, December 29, 2011

Just got this email announcement and I thought I would share. As many know, in the aftermath of the pepper spray incident, whether you support the UC Davis Chancellor or not, it was pretty clear that communications regarding the incident were, well, poor at best. Hopefully this will improve things. Of course, action is more important than communication --- but I am glad to see the Chancellor responding to communication issues ---

Dear Colleagues, I write to inform you about additional actions that I am taking immediately to strengthen Strategic Communications. These steps will help us address needs and challenges facing UC Davis today while preparing us to take advantage of opportunities that lie ahead.

I was starting to compile a Top 10 list of best humorous Science-related videos of the year. And I got stuck on #1 because it is so so so good. But I was able to find some others I liked (and listed them in no particular order)... so here goes. If you know of other good ones please post/tweet ...

1. Bad Project video from the Zheng lab. This is simply awesome.

2. Top 10 quirky science tricks for parties. I found out about this from Twitter ... and it is very good.

I thought I would write a letter to you to help guide you in how to apply for a position in my lab. Here are some suggestions for things that really help out - based on real emails I note ...

Describe your interests by copying text from my web site. This shows that you are not only able to read, but also able to either copy directly or retype what you have read. It is very appealing.

Get my name or institution wrong in some way. This shows that you are likely being industrious in applying for lots of jobs.

Include attachments that do not open on Macs. Screw Steve Jobs and all of his fans.

Send the same email multiple times - once to Prof. Eisen at UC Davis, once to Dr. Eisen at JGI, and once to Prof. Eisen from the "Genome Center at UC Davis." Repetition is an important literary technique.

Refer to the "reputation" of my group without saying anything specific about what interests you. I love things based on reputation alone.

Describe your background as very relevant to our work and then say that you too have focused extensively on microarray based studies of gene expression (I love stealing candidates whose original goal was to work in my brother's lab).

Have no publications but a list of more than 10 as "in preparation".

Include viruses in attachments - as I am interested in evolution of microbes this is appealing.

Express an interest in biological weapons and biological defense and be from a terrorism sponsoring country.

Have the original email message be more than four pages long with dozens of questions for me about my institution and my open positions.

Thursday, December 22, 2011

There was an issue with the set up of the email address for the Special Committee that has now been corrected by IT. If you sent an email to the committee prior to Wednesday December 21st, we request that you send it again. Sorry for the inconvenience.

Wednesday, December 21, 2011

The must have job of 2012 - a faculty position in my Department at UC Davis. It is a GREAT department both scientifically (UC Davis is consistently ranked as having one of the best Evolution/Ecology programs in the country) and personally (the faculty, staff and students are great to be around). See below for more information. I am happy to give people any details of the Department, School, campus, etc if you are interested.

EVOLUTION OF ORGANISMAL DIVERSITY, UNIVERSITY OF CALIFORNIA, DAVIS

The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT Professor level, with the possibility of ASSOCIATE appointment with tenure. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields.

They should have a strong record of integrative approaches to the evolution of organismal diversity. We seek candidates with expertise in the organismal biology/natural history of a multicellular group, and whose research uses genomic data in an explicitly phylogenetic context to address questions in macroevolution, ecology, behavior and/or development. The successful candidate will be expected to teach in the department's undergraduate program and in the Population Biology Graduate Group and should be committed to departmental service.

Applicants should submit materials online at this site which contains additional information about the position. Materials required include: curriculum vitae, description of current and projected research, summary of teaching interests and experience, and up to five publications. Applicants should also provide the information requested for three referees. Once entered, referees will be prompted by email with upload instructions for their letters.

Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by February 6, 2012, to assure full consideration.

The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

For those interested in outbreaks of infectious diseases (which I assume is actually everyone in the world) - there is a nice resource out there called PROMED-MAIL. It comes from the International Society for Infectious Diseases and it catalogs some recent stories from around the world on outbreaks. It is worth checking out. And if you like it, they are trying to raise some funds to keep it going with an Internet-A-Thon so consider donating ...

Just got an email about a meeting of potential interest and thought I would share:

It is my pleasure to announce that registration and abstract submission for the 16th Evolutionary Biology Meeting at Marseilles, September 18-21, 2012, is open. Please visit the web site of the meeting http://sites.univ-provence.fr/evol-cgr where you will find all relevant information.

In 2006 when I had just moved to UC Davis from TIGR, I was on a Southwest flight from Sacramento to (I think) Arizona. The person sitting next to me and I did the normal chit chat - what do you do? where are you going? etc. And the conversation became fascinating. The person sitting next to me was Mike Lagrone - a farrier (I forget people's names frequently ten minutes after meeting them - but his name I remember even today, so he clearly made an impression). He travelled around the West helping take care of people's horses. (I note - I think more information about him is here Mike Lagrone | EquiMed - Horse Health Matters).

It discusses the development of international annotation standards at NCBI (The National Center for Biotechnology Information) in collaboration with others. Note - the paper is Open Access.

Their abstract:

The promise of genome sequencing was that the vast undiscovered country would be mapped out by comparison of the multitude of sequences available and would aid researchers in deciphering the role of each gene in every organism. Researchers recognize that there is a need for high quality data. However, different annotation procedures, numerous databases, and a diminishing percentage of experimentally determined gene functions have resulted in a spectrum of annotation quality. NCBI in collaboration with sequencing centers, archival databases, and researchers, has developed the first international annotation standards, a fundamental step in ensuring that high quality complete prokaryotic genomes are available as gold standard references. Highlights include the development of annotation assessment tools, community acceptance of protein naming standards, comparison of annotation resources to provide consistent annotation, and improved tracking of the evidence used to generate a particular annotation. The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved functions, is an historic milestone. The use of these standards in existing genomes and future submissions will increase the quality of databases, enabling researchers to make accurate biological discoveries.

The paper refers extensively to workshops held by NCBI on genome annotation and gives a link to a page from NCBI with additional information about these workshops.

Now - never mind the extensive use of the term prokaryote in the paper ... the paper has got a wealth of information and tidbits worth checking out.

Friday, December 16, 2011

This message provides notice of two impending ballots, as required by Davis Division Bylaw 17: http://academicsenate.ucdavis.edu/cerj/manual/dd_bylaws.cfm#17-. You have received this notice as a voting member of the Davis Division of the Academic Senate. The Davis Division received at least 50 valid signatures with each petition, requiring initiation of a formal notice and electronic ballot. More information, including the method for gathering pro and con statements and the voting period, will be distributed on January 9, 2012. The petitions are summarized below:

1) Petition received on December 6, 2011, requests a vote regarding a lack of confidence in the leadership of Chancellor Katehi, with the result of the vote to be communicated to the Board of Regents and UC President.

I am posting here a wrap up of my notes from the National Academy of Sciences Institute of Medicine Forum on Microbial Threats meeting on Improving Food Safety Through One Health I just attended. I made a little "story" via Storify and that is what I am embedding below. More comments to follow I hope but wanted to get this out there.

Thursday, December 15, 2011

Update2 - 12/22 - Data available here. Thanks to the authors for clearing things up quickly.
Update1 - 12/19 - Data for this paper seems to be unavailable - not sure why - but looking into this after a TWEET from Karen Cranston. The paper says data is available at: http://nypg.bio.nyu.edu/main/ but I could not find any there. Note - this is one reason that all data sets should be made available at the journal or third party sites.Original post:

Just got this email. On the one hand it is nice to see that NSF is not keeping around programs when they may no longer be needed. On the other hand, this somehow seemed melancholy ...

Dear Colleague,

The Cyber-Enabled Discovery and Innovation program has demonstrated the value of interdisciplinary computational and data-enabled science and engineering. Increasingly, this research approach is being integrated into new and continuing NSF programs and solicitations. As of fiscal year 2012, proposals will no longer be accepted by the CDI program.

Went to the Smithsonian Museum of Natural History. Did something there. And got this email regarding it with a picture attached. Explanation is below. Though I think I probably should have taken off my glasses ...

Dear Visitor,

Congratulations! You have been transformed into a Homo neanderthalensis, one of the closest relatives of modern humans. Your picture is attached.

Then I uncompressed it and tried to run it. When I opened the index.html file in Chrom I got a message saying it only worked in Firefox. So then I opened it in Firefox and I got an error saying it only worked in newer versions of Firefox. So I downloaded the latest version of Firefox and then finally the tool opened. I then followed the simple tutorial they have provided and Voila I was up and running in a few minutes

Completely cool. Going to definitely have to try this out with our own site-variable microbial data.

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

Saturday, December 10, 2011

Just got a pointer to this by email and thought some would be interested (not endorsing everything that is there but it is definitely worth a look - the Fact Sheet they are annotating rubbed me the wrong way too).

In the piece Zimmer discusses the issue of who owns your microbiome. This can be considered an extension of the concept of "Who owns your cells?" such as has been discussed in the context of Rebecca Skloot's HELA book.

My favorite line(s):

Monitoring the bacteria flushed into the sewer system of a town, for instance, might reveal a lot about the entire town’s health. But a regulation requiring permission from every resident of the town would stop the study dead in its tracks

Personally I think none of us own our microbes - since we get them from the world around us and likely share them with millions of others. It would be akin to saying we own genes found in all humans. But there very well may be some person specific alleles in microbes that could in a way be akin to person specific cell lines. Not sure.

Anyway - I think I am going to name all my microbes as a first step in protecting my rights to them ...

Just found out about this new kids book about Antarctica: Antarctic Adventure. Hat tip to Jeff Hoffman, a friend who has been on many many scientific field adventures.

From the book web site:

Antarctic Adventure is the story of author/scientist Mak Saito's research expedition to the Southern Continent. The book is targeted at children age 3 - 7. Simple text and stunning photographs highlight the adventure elements of fieldwork in the Antarctic (helicopters, snow storms, wildlife). Children learn where Antarctica is, what algae are, what glaciers look like, and the names of several different whales and penguins. More generally, they get a sense of what it means to do scientific fieldwork. A "Dear Reader" section at the end of the book goes into more detail about the expedition's research goals, which involve the importance of algae in global biogeochemical cycles.

I have just bought a copy ... will let people know more when I get it but I am guessing it is going to be good ...

I had posted this to twitter a while ago but not here. There is a report that came out from the American Academy of Microbiology from a Workshop in which I participated. The report is on "The Rare Biosphere, 2011" and it discusses some of the issues associated with the long tail of rare organisms that might exist, especially microbes. It is worth a look.

From their page:

The microbial world represents the last truly unexplored frontier in the diversity of life on Earth. New environmental sampling technologies have revealed a wealth of rare microbial species in the soil, ocean, even our own bodies that were effectively cloaked from previous sampling methods by more abundant species. Dubbed the rare biosphere, these microbial species, while individually rare, collectively account for more than 75% of the biomass of some microbial communities, yet little is known about them. This rare biosphere represents a treasure trove of genetic novelty that may possess numerous unique bioprocesses and biomaterials. These rare species may play keystone roles in microbial communities and act as a reservoir of genetic diversity. But how can scientists effectively study the rare biosphere? In April 2009 the American Academy of Microbiology convened a colloquium to explore this question. Based on that colloquium, this report analyzes the current state of study of the rare biosphere and identifies where gaps in knowledge exist. The report concludes that the Herculean task of studying the rare biosphere requires an international collaborative effort and additional environmental sampling, coupled with a focus on advancing sequencing and data analysis technologies. With less than 1% of microbial species able to be grown in the laboratory, the prospects of new discoveries in the rare biosphere seem as vast as microbial diversity itself.

Just got this digitized. One of my proudest moments. In 1997 I received the Walter J. Gores Award for excellence in teaching for my work on the "SME Core" at Stanford. The SME Core was a new way to teach Science, Math and Engineering for non science majors.

The SME Core was an initiative coordinated in part by then Stanford Provost Condoleezza Rice. I worked with her office on and off for 3 years to help get the SME Core program up and running. (I note - whatever you think of her now - at the time I really really liked her - she was great to interact with, brilliant, and I think inspired in pushing this SME program).

It discusses the story of the discovery of the first hydrothermal vent oases back in 1977. I note this is near and dear to my heart. I worked as an undergraduate and then after graduating in Colleen Cavanaugh's lab at Harvard on chemosynthetic symbioses. And then amazingly I got to go on the 2002 deep sea cruise celebrating the 25th anniversary of the discovery of the vents. On that cruise Rosebud (mentioned in this article) was discovered.

And today was the day. It was a very hectic day for me. AM kid related duties. Then I dropped off two pairs of broken glasses to get soldered (one of which had broken on the day of the major post-pepper spray rally at UC Davis. Then off to lab where I had only a short period of free time before lab meeting (alas, unlike last week, this meeting was indoors). And then off to the meeting with the Chancellor. Here are some notes from that meeting --- more of a stream of consciousness than detailed notes in many cases but hopefully this will give a gist of how the meeting went.

Wednesday, December 07, 2011

OMG - for crying out loud. In the following story Billion-year-old Bacteria Could be Medical Goldmine Fox News discusses studies of marine cyanobacteria at the University of Florida. It is so wrong in so many ways I do not know where to begin. Watch the video first for layers of trouble. Then, if you dare, read the article. Among the painful parts:

"Bits & bites is a new lunch club that aims to meet once a week at UC Davis and talk about various aspects of sequence analysis. The idea is to gather together people in a very informal environment and share expertise on various subjects relating to bioinformatics and genomics."

More detail from the site:

The plan will be to meet on Thursdays between 12:00 and 1:00 at various venues on the UC Campus, possibly including the Genome Center, and Life Sciences Addition – as well as possible forays into Davis. Occasionally – maybe once a month – we would try to host an invited speaker to give deeper insights into a specific topic.

To find out more details please join the bits & bites mailing list (a low traffic list which will mostly be used to announce the venue and discussion topics each week).

The UC Davis Genome Center will be holding an Omics Office Hour from 9:00-10:00am each month in Room 5206 GBSF on the Davis campus. These drop-in sessions are open to anyone with questions regarding Genomics, Epigenomics and Gene Expression, Proteomics, Metabolomics, Network Biology and Bioinformatics.

The mission of the Genome Center is to facilitate your "omics" research at UC Davis. Genome Center staff and faculty will be on hand for consultation in a friendly, informal setting. If you have ideas that you would like to explore, we would be happy to discuss it as well as the possibility of pilot grants.